Pinto Corujo, Marco Antonio (2019) Analysis of secondary structure of proteins by vibrational spectroscopy and self-organizing maps. PhD thesis, University of Warwick.

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Abstract

Antibodies are proteins produced by the immune system and one of the top biopharmaceutical market types due to their applications in oncology therapy among others4. As any other protein, their functionality depends on the preservation of their native form which, under certain stressing conditions, can undergo changes at different structural levels and thus loss of their activity. Although mass spectrometry is a powerful technique for primary structure determination, it often fails to give information at higher order levels. In this project we explored the possibilities of vibrational spectroscopic techniques as a tool kit to help ensure the integrity and batch to batch reproducibility in antibody manufacture.

Infrared (IR) and Raman spectra are well known to contain bands (Amide I, II and III) with shapes that correlate to secondary structure (SS)6,7. Unlike Circular Dichroism (CD) (the most well-established technique for secondary structure analysis8), IR and Raman spectroscopy allow much wider ranges of optical density which makes the analysis of complex pharmaceutical samples more feasible. However, the data processing and extraction of this information are ambiguous and, in many cases, limited by spectral noise and water absorption in IR and fluorescence in Raman.

In this work, data sets of proteins with known SS were collected in both solid and aqueous state by Raman, IR and Raman Optical Activity and used along a neural network algorithm called Self-Organizing Maps (SOMspec) for SS prediction of proteins. It was found that Raman spectroscopy provides the best predictions followed by IR based on the shape of the amide I band. Although the ROA amide I of proteins has also been reported in the literature to correlate to SS content, we failed to predict SS structure by ROA-SOM based on this band. More work needs to be carried out in the future to attempt to predict SS based on the ROA amides II and III instead.

Item Type:	Thesis or Dissertation (PhD)
Subjects:	Q Science > QD Chemistry
Library of Congress Subject Headings (LCSH):	Proteins -- Structure, Two-dimensional electronic-vibrational spectroscopy, Self-organizing maps
Official Date:	September 2019
Dates:	Date Event September 2019 UNSPECIFIED
Institution:	University of Warwick
Theses Department:	Department of Chemistry
Thesis Type:	PhD
Publication Status:	Unpublished
Supervisor(s)/Advisor:	Rodger, Alison ; Chmel, Nikola
Sponsors:	AstraZeneca (Firm) ; Engineering and Physical Sciences Research Council
Extent:	xx, 200 leaves : illustrations
Language:	eng

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